seq.findPosition(sg.getStartRes()) + "\t"\r
+ seq.findPosition(sg.getEndRes()) + "\t"\r
+\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ seq.getSequence(sg.getStartRes(),\r
sg.getEndRes() + 1) + "\n");\r
}\r
\r
return;\r
}\r
\r
+\r
SequenceGroup sg = viewport.getSelectionGroup();\r
+ boolean allSequences = false;\r
+ if(sg.sequences.size()==viewport.alignment.getHeight())\r
+ allSequences = true;\r
+\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+\r
if (seq.getSequence().length() < 1)\r
{\r
viewport.getAlignment().deleteSequence(seq);\r
\r
int start=0, end = viewport.alignment.getWidth();\r
\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size()>0)\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
}\r
j++;\r
}\r
- while(j < end);\r
+ while(j < end && j < jSize) ;\r
}\r
\r
viewport.updateConservation();\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
-\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org");\r
-\r
+ jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalView - Release 2.0", 200, y += fh);\r
+ g.drawString("JalView - Release 2.01", 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
x, y += fh * 2);\r